see my comments inserted below
On Mon, Oct 5, 2020 at 11:31 AM Asaf Farhi <asaf.farhi.gmail.com> wrote:
> Dear all,
>
> My name is Asaf and I'm a postdoc at Creol, UCF.
>
> I would be happy to consult with you regarding the choice of force field
> for proteins.
> I have read in the manual that the recommended force field for proteins is
> ff14SB.
>
> I have a few questions and I would really appreciate your help:
> 1. What does SB stand for?
>
SB stands for Stony Brook, my home institution. All of the protein models
from my lab are indicated with the "SB"
> 2. Can the CMAP parameters be changed (manually) in free energy
> calculations with Gromacs?
>
I don't know how Gromacs handles CMAPs, it may be better to ask Gromacs
developers. Note that ff14SB does not include CMAPs, so this may not
matter. ff19SB includes CMAPs, and ot my knowledge this is not yet
implemented in Gromacs since we use different CMAPs for different amino
acids.
> 3. What is the recommended force field without CMAP?
>
ff14SB does not use CMAPs
> 4. Are Amber99 or Amber99sb*-ILDN recommended?
>
Amber99 (really should be called ff99) is not recommended, it is very old
and should no longer be used.
ff99SB*-ILDN is more recent, but my recommendation would be to use ff14SB
instead. Of course others may have good experience with ff99SB*-ILDN as
well. It included some backbone and sidechain updates to our ff99SB model,
but ff14SB has a more extensive refitting of side chain parameters (in
addition to a small backbone adjustment).
> Thank you for your help,
> Best regards,
> Asaf
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>
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Received on Mon Oct 05 2020 - 09:00:04 PDT
